The Buccaneer software for automated model building.: 1.: Tracing protein chains

A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C-alpha positions. This function is applied both in the location of a few promising `seed' positions in the map and to grow those initial C-alpha positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.